.travis.yml

language: python
python:
  - "3.6"
install:
  - sudo apt-get update
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a

  # Replace dep1 dep2 ... with your dependencies
  - conda env create -f environment.yml
  - source activate multifactorial-immune-response-env

script:
  - snakemake process_data
  - travis_wait 30 snakemake train_model -j 2
  - snakemake biomarkers_and_dcb
  - snakemake reduce_permutation_test
  - snakemake plot

deploy:
  provider: pages
  skip-cleanup: true
  github-token: $GITHUB_TOKEN  # Set in travis-ci.org dashboard, marked secure
  keep-history: true
  local-dir: output/en/figs
  fqdn: multifactorial-immune-response.lrgr.io
  on:
    branch: master